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General

Can I combine BIDS and neurodata without border (NWB)?

BIDS and NWB are compatible.

An NWB data file is an allowed format in the iEEG-BIDS data structure. This means that one subject (AAA) with a session (BBB) can have a BIDS folder with raw iEEG data in NWB format:

/sub-AAA/ses-BBB/ieeg/sub-AAA_ses-BBB_task-rest_ieeg.nwb

The same subject can have another session (CCC) with raw fMRI data in BIDS:

/sub-AAA/ses-CCC/func/sub-AAA_ses-CCC_task-rest_bold.nii.gz

How can I cite BIDS?

See the specification website for the main publications related to BIDS and its extensions.

BIDS references are centralized in a zotero group.

How do I convert my data to BIDS?

We strongly recommend you pick a BIDS converter to help you convert your data.

A list of converters can be found on the BIDS website

Also look at the list of tutorials and information about conversions.

How should I organize data for hyperscanning data?

Hyperscanning is simultaneous fMRI with multiple subjects (see this paper).

  • See this issue in the bids specification repository for typical hyperscanning data.

See an example below with fMRI data:

sub-01/
    ses-dyadic1/
        func/
            sub-01_ses-dyadic1_*
sub-02/
    ses-dyadic1/
        func/
            sub-02_ses-dyadic1_*
sub-03/
    ses-dyadic2/
        func/
            sub-03_ses-dyadic2_*
sub-04/
    ses-dyadic2/
        func/
            sub-04_ses-dyadic2_*

See an example below with fMRI data:

sub-S001/
    ses-1/
        func/
            sub-S001_ses-1_task-video_acq-dyad001_bold.nii.gz
    ses-2/
sub-S002/
    ses-1/
        func/
            sub-S002_ses-1_task-video_acq-dyad001_bold.nii.gz
    ses-2/
sub-S003/
    ses-1/
        func/
            sub-S003_ses-1_task-video_acq-dyad002_bold.nii.gz
    ses-2/

How to import Excel files to TSV file?

See our sections on TSV files for more information.

See also this bids tool to import and export a participants.tsv file: bids-matlab-tools

How to specify the micro sign in MATLAB?

BIDS requires physical units to be specified according to the SI unit symbol and possibly prefix symbol (for example: mV, μV for milliVolt and microVolt).

The symbol used to indicate µ has unicode U+00B5, which is in MATLAB:

char(181)

or

native2unicode(181, 'latin1')

I had to split the testing of one of my participants across 2 days, should I use 2 different session folders to organize the data of that participant?

No. The session level in the BIDS folder hierarchy can be used to group data that go "logically" together: this means that you can put in the same session folder data that were acquired on different days, but that are "linked" to one another in a way that make sense to how you want to organize your data.

If you want to keep track of what data was acquired when you can use the scans.tsv files.

For some examples, see this issue in the bids-starter kit.

If you deal with EEG data, you may want to read this comment in another issue as well before considering combining recordings acquired on different occasions within the same session folder.

Is there a machine readable version of the BIDS specification?

Yes. The BIDS specification exist as a schema. The BIDS schema is a machine readable representation of the BIDS Standard. It is (by and large) the BIDS Specification, but written in a declarative form.

The BIDS schema is available in two machine readable formats:

A light-weight introduction to the schema can be found here.

A full description of the schema can be found on this website where you will also find the documentation for the python package to interact with the schema, bidsschematools.

Is your data type not covered in the current BIDS specification?

BIDS extensions proposals (BEPs) aim to extend the BIDS specification to new data types. A list of extensions ongoing and completed proposals can be found here.

Guidelines for contributing to these extensions or starting your own can be found in the BIDS Extension Proposals Guide.

If only part of your data is covered under BIDS, an option to allow additional files currently not covered in BIDS to pass the validator is the .bidsignore file, which works just like .gitignore. It allows you to list all the files (or directories, with wildcards) that are not BIDS compliant and should be ignored by the validator. Of course you should still try to adhere to upcoming BEPs and the general BIDS philosophy for file names and metadata where possible, but this gives a little extra flexibility.

What does [this word] mean?

We're building a glossary to de-jargonise some of the terms you need to know to work with data in BIDS format. Check it out here.

What is a json file?

You can find more information about json (and tsv) files in the Metadata-file-formats page.

What liense should I choose for my dataset?

If you want to know more about what license to choose for your dataset, see the turing way page dedicated to this topic.

If you plan to put your dataset on openneuro, you should use a CC0 or a PDDL license as explained in their FAQ.

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